See this image for example. The red flasher is one of the Neo-docklights flashers, so it is actually located between the player and the station.

This happens with a modified version of Neo-docklights that adds a phase parameter to the flashers, but Hoqlinq has also spotted anomalies with the unmodified version. Modified OXP and slightly more info in this thread.

This is present on the latest master, running under Windows Seven and NVidia graphic card.

It is the same in the original and the modified oxp.
When you're closer to the station than about 4200m, the flashers are clipped by the station. (You still see them one at a time when they're really close as you fly through them.)

I believe this is what happens:
All entities are drawn from farthest to nearest. But sub-entities are drawn along with their parent. The dock light is a long string of sub-entities. The parent is positioned farthest from the station, close to the buoy. So when you're closer to the station than to the dock light string parent entity, the lights are drawn earlier than the station. (Although this does not explain the part where you still see them when very close.)

I tested this by positioning the parent right in front of the station and pointing the string outward. This fixes the clipping / drawing order issue.